A scalable filtration-based method for isolating exomeres and other nanoscale extracellular particles

Abstract

Extracellular particles, including extracellular vesicles (EVs) and non-vesicular extracellular particles (NVEPs), enable intercellular communication by transferring regulatory miRNAs and other biomolecules. While EVs have been studied for drug delivery, NVEPs remain relatively unexplored. Exomeres, a recently discovered class of NVEPs enriched in RNAi proteins, preferentially carry miRNAs and deliver them to cells more effectively than EVs, underscoring their potential as vehicles for therapeutic RNAs. One current limitation to studying and applying exomeres for therapeutic RNA delivery is the shortage of scalable, cost-effective, and rapid isolation methods. Here, we investigated whether tangential flow filtration (TFF), a common bioseparation approach that separates species by size, would effectively isolate exomeres from conditioned media with comparable purity and identity to those isolated by differential ultracentrifugation. TFF successfully isolated exomeres that were enriched in RNAi components including AGO2, HSP90AB1, and a unique set of miRNAs not abundant in EVs. Remarkably, exomere miRNAs were resistant to nuclease degradation even after treatment with protease and surfactant, suggesting that exomeres are highly stable, non-vesicular complexes with potentially extended circulating half-lives. Together, our results establish TFF as an efficient method for isolating exomeres, and further demonstrate that TFF could be applied in a bioprocess for exomere-based RNA therapeutics production. This study is also the first to demonstrate that exomere miRNAs are highly resistant to nuclease degradation, suggesting that exomeres could complement and potentially outperform current clinical standards for RNA delivery.